All Stories

  1. EPIG-Seq for identifying co-expressed genes from RNA-Seq data

    Article • BMC Genomics, March 2016, Springer Science + Business Media

    Pierre R Bushel

  2. Abstract 1972: LIN28 gene targets are key mediators of breast cancer disease processes

    Article • Cancer Research, August 2015, American Association for Cancer Research (AACR)

    Pierre R Bushel

  3. LIN28A modulates splicing and gene expression programs in breast cancer cells

    Article • Molecular and Cellular Biology, July 2015, ASM Journals

    Pierre R Bushel

  4. Technical guide for applications of gene expression profiling in human health risk assessment of environmental chemicals

    Article • Regulatory Toxicology and Pharmacology, July 2015, Elsevier

    Dr Russell S Thomas, Pierre R Bushel

  5. Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity

    Article • Frontiers in Genetics, February 2015, Frontiers

    Pierre R Bushel

  6. Novel Roles for Notch3 and Notch4 Receptors in Gene Expression and Susceptibility to Ozone-Induced Lung Inflammation in Mice

    Article • Environmental Health Perspectives, February 2015, Environmental Health Perspectives

    Pierre R Bushel

  7. Development of Phenotypic and Transcriptional Biomarkers to Evaluate Relative Activity of Potentially Estrogenic Chemicals in Ovariectomized Mice

    Article • Environmental Health Perspectives, January 2015, Environmental Health Perspectives

    Pierre R Bushel, Sylvia Hewitt

  8. The rat microRNA body atlas: Towards understanding serum microRNA changes and their utilisation as biomarkers of specific organ toxicity

    Article • Toxicology Letters, September 2014, Elsevier

    Pierre R Bushel

  9. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

    Article • Nature Biotechnology, August 2014, Nature

    Pierre R Bushel

  10. Dynamic expression of 3′ UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: Implications in gene expression profiling

    Article • Gene, September 2013, Elsevier

    Pierre R Bushel

  11. Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification

    Article • Cancer Informatics, August 2013, Libertas Academica, Ltd.

    Pierre R Bushel

  12. Gene Expression in Uterine Leiomyoma from Tumors Likely to Be Growing (from Black Women over 35) and Tumors Likely to Be Non-Growing (from White Women over 35)

    Article • PLoS ONE, June 2013, PLOS

    Pierre R Bushel

  13. p53 integrates host defense and cell fate during bacterial pneumonia

    Article • The Journal of Cell Biology, May 2013, Rockefeller University Press

    Pierre R Bushel

  14. p53 integrates host defense and cell fate during bacterial pneumonia

    Article • The Journal of Experimental Medicine, April 2013, Rockefeller University Press

    Pierre R Bushel

  15. Widespread Exonization of Transposable Elements in Human Coding Sequences is Associated with Epigenetic Regulation of Transcription

    Article • Transcriptomics Open Access, January 2013, OMICS Publishing Group

    Pierre R Bushel

  16. Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes

    Article • BMC Systems Biology, January 2013, Springer Science + Business Media

    Pierre R Bushel

  17. Transcriptional responses to loss of RNase H2 in Saccharomyces cerevisiae

    Article • DNA Repair, December 2012, Elsevier

    Pierre R Bushel

  18. Sources of variance in baseline gene expression in the rodent liver

    Article • Mutation Research/Genetic Toxicology and Environmental Mutagenesis, August 2012, Elsevier

    Pierre R Bushel

  19. Research Resource: Whole-Genome Estrogen Receptor α Binding in Mouse Uterine Tissue Revealed by ChIP-Seq

    Article • Molecular Endocrinology, May 2012, Endocrine Society

    Pierre R Bushel, Sylvia Hewitt

  20. Population Differences in Transcript-Regulator Expression Quantitative Trait Loci

    Article • PLoS ONE, March 2012, PLOS

    Pierre R Bushel

  21. The Impact of Classification of Interest on Predictive Toxicogenomics

    Article • Frontiers in Genetics, January 2012, Frontiers

    Pierre R Bushel

  22. Identification of Identical Transcript Changes in Liver and Whole Blood during Acetaminophen Toxicity

    Article • Frontiers in Genetics, January 2012, Frontiers

    Pierre R Bushel

  23. Maximizing biomarker discovery by minimizing gene signatures

    Article • BMC Genomics, January 2011, Springer Science + Business Media

    Pierre R Bushel

  24. The Evolution of Bioinformatics in Toxicology: Advancing Toxicogenomics

    Article • Toxicological Sciences, December 2010, Oxford University Press (OUP)

    Pierre R Bushel

  25. Development of gut microbiota in infants not exposed to medical interventions

    Article • Apmis, October 2010, Wiley

    Pierre R Bushel

  26. CLUSTERING OF GENE EXPRESSION DATA AND END-POINT MEASUREMENTS BY SIMULATED ANNEALING

    Article • Journal of Bioinformatics and Computational Biology, February 2009, World Scientific Pub Co Pte Lt

    Pierre R Bushel

  27. Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007)

    Article • BMC Proceedings, January 2009, Springer Science + Business Media

    Pierre R Bushel

  28. Discernment of possible mechanisms of hepatotoxicity via biological processes over-represented by co-expressed genes

    Article • BMC Genomics, January 2009, Springer Science + Business Media

    Pierre R Bushel

  29. Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle

    Article • BMC Systems Biology, January 2009, Springer Science + Business Media

    Pierre R Bushel

  30. Global Transcriptome and Deletome Profiles of Yeast Exposed to Transition Metals

    Article • PLoS Genetics, April 2008, PLOS

    Pierre R Bushel

  31. Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants

    Article • BMC Genomics, January 2008, Springer Science + Business Media

    Pierre R Bushel

  32. Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories

    Article • BMC Genomics, January 2008, Springer Science + Business Media

    Pierre R Bushel

  33. Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype

    Article • Genome Biology, January 2008, Springer Science + Business Media

    Pierre R Bushel

  34. Identification of Primary Transcriptional Regulation of Cell Cycle-Regulated Genes upon DNA Damage

    Article • Cell Cycle, April 2007, Taylor & Francis

    Pierre R Bushel

  35. Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes

    Article • BMC Systems Biology, January 2007, Springer Science + Business Media

    Pierre R Bushel

  36. Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes

    Article • BMC Bioinformatics, January 2007, Springer Science + Business Media

    Pierre R Bushel

  37. Toxicogenomics

    Article • March 2006, Taylor & Francis

    Pierre R Bushel

  38. Profiles of Global Gene Expression in Ionizing-Radiation–Damaged Human Diploid Fibroblasts Reveal Synchronization behind the G1 Checkpoint in a G0-like State of Quiescence

    Article • Environmental Health Perspectives, December 2005, Environmental Health Perspectives

    Pierre R Bushel

  39. PAGE: phase-shifted analysis of gene expression

    Article • Bioinformatics, December 2005, Oxford University Press (OUP)

    Pierre R Bushel

  40. The Chemical Effects in Biological Systems (CEBS) Knowledge Base

    Article • May 2005, Wiley

    Pierre R Bushel

  41. SYSTEMATIC VARIATION NORMALIZATION IN MICROARRAY DATA TO GET GENE EXPRESSION COMPARISON UNBIASED

    Article • Journal of Bioinformatics and Computational Biology, April 2005, World Scientific Pub Co Pte Lt

    Pierre R Bushel

  42. Databases for Toxicogenomics

    Article • January 2005, Wiley

    Pierre R Bushel

  43. Integration of clinical and gene expression endpoints to explore furan-mediated hepatotoxicity

    Article • Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, May 2004, Elsevier

    Pierre R Bushel

  44. Database Development in Toxicogenomics: Issues and Efforts

    Article • Environmental Health Perspectives, January 2004, Environmental Health Perspectives

    Pierre R Bushel

  45. DATABASE DEVELOPMENT IN TOXICOGENOMICS: ISSUES AND EFFORTS

    Article • Environmental Health Perspectives, January 2004, Environmental Health Perspectives

    Pierre R Bushel

  46. ATM-Dependent and -Independent Gene Expression Changes in Response to Oxidative Stress, Gamma Irradiation, and UV Irradiation

    Article • Radiation Research, September 2003, Radiation Research Society

    Pierre R Bushel

  47. Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiation

    Article • Molecular Carcinogenesis, June 2003, Wiley

    Pierre R Bushel

  48. Genomic interrogation of mechanism(s) underlying cellular responses to toxicants

    Article • Toxicology, December 2002, Elsevier

    Pierre R Bushel

  49. Systems Toxicology and the Chemical Effects in Biological Systems (CEBS) Knowledge Base

    Article • Environmental Health Perspectives, November 2002, Environmental Health Perspectives

    Pierre R Bushel

  50. Alterations in apoptotic signaling in human idiopathic cardiomyopathic hearts in failure

    Article • AJP Heart and Circulatory Physiology, September 2002, American Physiological Society

    Pierre R Bushel

  51. Methapyrilene Toxicity: Anchorage of Pathologic Observations to Gene Expression Alterations

    Article • Toxicologic Pathology, July 2002, SAGE Publications

    Pierre R Bushel

  52. Gene expression pattern recognition algorithm inferences to classify samples exposed to chemical agents

    Article • June 2002, SPIE

    Pierre R Bushel

  53. Regulation of DNA Replication Fork Genes by 17β-Estradiol

    Article • Molecular Endocrinology, June 2002, Endocrine Society

    Pierre R Bushel

  54. Computational selection of distinct class- and subclass-specific gene expression signatures

    Article • Journal of Biomedical Informatics, June 2002, Elsevier

    Pierre R Bushel

  55. Methapyrilene Toxicity: Anchorage of Pathologic Observations to Gene Expression Alterations

    Article • Toxicologic Pathology, June 2002, SAGE Publications

    Pierre R Bushel

  56. Systems Toxicology and the Chemical Effects in Biological Systems (CEBS) Knowledge Base

    Article • Environmental Health Perspectives, January 2002, Environmental Health Perspectives

    Pierre R Bushel

  57. Assessing Gene Significance from cDNA Microarray Expression Data via Mixed Models

    Article • Journal of Computational Biology, November 2001, Mary Ann Liebert Inc

    Pierre R Bushel

  58. Progress in the Application of DNA Microarrays

    Article • Environmental Health Perspectives, September 2001, JSTOR

    Pierre R Bushel

  59. Progress in the Application of DNA Microarrays

    Article • Environmental Health Perspectives, August 2001, Environmental Health Perspectives

    Pierre R Bushel

  60. Combination of functional genomics approaches and microarray analyses to define candidate senescence genes

    Article • Nature Genetics, April 2001, Nature

    Pierre R Bushel

  61. ATM-dependent responses to DNA-damaging agents

    Article • Nature Genetics, April 2001, Nature

    Pierre R Bushel

  62. Discovery in toxicology: Mediation by gene expression array technology

    Article • Journal of Biochemical and Molecular Toxicology, January 2001, Wiley

    Pierre R Bushel

  63. Discovery in toxicology: Mediation by gene expression array technology

    Article • Journal of Biochemical and Molecular Toxicology, January 2001, Wiley

    Pierre R Bushel

  64. Principal Variance Components Analysis: Estimating Batch Effects in Microarray Gene Expression Data

    Article • Wiley

    Pierre R Bushel